Align alpha-ketoglutarate permease (MHS family) (characterized)
to candidate HSERO_RS15670 HSERO_RS15670 major facilitator transporter
Query= reanno::pseudo5_N2C3_1:AO356_17790 (439 letters) >FitnessBrowser__HerbieS:HSERO_RS15670 Length = 427 Score = 256 bits (654), Expect = 1e-72 Identities = 146/391 (37%), Positives = 215/391 (54%), Gaps = 5/391 (1%) Query: 11 SAAVPARERTTASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKVFFPKGDTTAQLLNTA 70 + A P + T ++I S S+GN +EW+D +Y AF++ AK FFP GD + LL T Sbjct: 4 NTAAPGADITHPQARRAIISSSIGNALEWFDILIYGAFAVVIAKQFFPTGDDSVSLLLTF 63 Query: 71 AIFAVGFLMRPIGGWLMGLYADRAGRKRALMASVYLMCFGSLIIALSPSYETIGVGAPIL 130 A F V F MRP+G ++G Y+DRAGRK ALM S+ LM G+ +IA PSY +IG+ AP Sbjct: 64 ATFGVSFFMRPLGAVVLGAYSDRAGRKAALMLSIMLMTVGTAMIAFMPSYASIGLLAPAG 123 Query: 131 LVFARLLQGLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQF 190 + +++QG S GGE+G+S +L E A RRGFFSS+Q + L+A VL Sbjct: 124 IALGKMIQGFSAGGEFGSSTAFLVEHA-PHRRGFFSSWQVASQGISLLLAALFGAVLNNM 182 Query: 191 LTTEQLYAWGWRIPFAIGALCAVVALYLRRGMEETESFTKKEKSKESAMRTLLRHPK-EL 249 LT EQL +WGWR+PF G L A +Y+RR ++E F + + + +R H K L Sbjct: 183 LTPEQLASWGWRVPFIFGLLIAPAGIYIRRHLDEAPEFKESSEKTNAPLRDTFAHQKMRL 242 Query: 250 MTVVGLTMGGTLAFYTYTTYMQKYLVNTVGM-SISDSTTISAATLFLFMCLQPVIGGLSD 308 + G + T++ Y + Y+ Y V +G+ + S +S A L +F+ P++G LSD Sbjct: 243 LIGAGSVIMATVSVY-LSLYIPTYAVKQLGLPAWSSFAAMSVAGLIMFIG-SPLVGALSD 300 Query: 309 KIGRRPILIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAEL 368 KIGR P +I L + T P+ L + L ++++ Y + + A++ Sbjct: 301 KIGRTPFMITSSALYIVLTYPMFVFLTNSPGFLQLLLLQTVIGVLMTMYFAAMPALLADI 360 Query: 369 FPTEIRALGVGLPYALTVSIFGGTAEYIALW 399 FP R G+ L Y + V+IFGG A I W Sbjct: 361 FPVATRGTGMSLAYNIAVTIFGGFAGLIITW 391 Lambda K H 0.326 0.138 0.416 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 492 Number of extensions: 25 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 439 Length of database: 427 Length adjustment: 32 Effective length of query: 407 Effective length of database: 395 Effective search space: 160765 Effective search space used: 160765 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory